| Previous changeset 4:6242cda7e278 (2015-05-07) Next changeset 6:6202ec8aab61 (2015-07-21) |
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Commit message:
planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c |
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modified:
tool_dependencies.xml tophat2_wrapper.xml tophat_macros.xml |
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| diff -r 6242cda7e278 -r 5c5517d2a9e9 tool_dependencies.xml --- a/tool_dependencies.xml Thu May 07 15:16:15 2015 -0400 +++ b/tool_dependencies.xml Thu May 14 09:39:04 2015 -0400 |
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| @@ -1,12 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="bowtie2" version="2.1.0"> - <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="bowtie2" version="2.2.5"> + <repository changeset_revision="39c07d717634" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="samtools" version="0.1.18"> - <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="tophat2" version="2.0.9"> - <repository changeset_revision="8549fd545473" name="package_tophat2_2_0_9" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="tophat" version="2.0.14"> + <repository changeset_revision="995175fb61c4" name="package_tophat_2_0_14" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
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| diff -r 6242cda7e278 -r 5c5517d2a9e9 tophat2_wrapper.xml --- a/tophat2_wrapper.xml Thu May 07 15:16:15 2015 -0400 +++ b/tophat2_wrapper.xml Thu May 14 09:39:04 2015 -0400 |
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| b'@@ -1,11 +1,10 @@\n-<tool id="tophat2" name="Tophat" version="0.7">\n+<tool id="tophat2" name="Tophat" version="0.9">\n <!-- Wrapper compatible with Tophat version 2.0.0+ -->\n <description>Gapped-read mapper for RNA-seq data</description>\n <version_command>tophat2 --version</version_command>\n <requirements>\n- <requirement type="package" version="0.1.18">samtools</requirement>\n- <requirement type="package" version="2.1.0">bowtie2</requirement>\n- <requirement type="package" version="2.0.9">tophat2</requirement>\n+ <requirement type="package" version="2.2.5">bowtie2</requirement>\n+ <requirement type="package" version="2.0.14">tophat</requirement>\n </requirements>\n \n <command>\n@@ -131,21 +130,21 @@\n \n <inputs>\n <conditional name="singlePaired">\n- <param name="sPaired" type="select" label="Is this library mate-paired?">\n+ <param name="sPaired" type="select" label="Is this single-end or paired-end data?">\n <option value="single">Single-end</option>\n <option value="paired">Paired-end (as individual datasets)</option>\n <option value="paired_collection">Paired-end (as collection)</option>\n </param>\n <when value="single">\n- <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>\n+ <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>\n </when>\n <when value="paired">\n- <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />\n- <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />\n+ <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" help="Must have Sanger-scaled quality values with ASCII offset 33" />\n+ <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads" help="Must have Sanger-scaled quality values with ASCII offset 33" />\n <expand macro="paired_parameters" />\n </when>\n <when value="paired_collection">\n- <param format="fastqsanger" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ paired reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />\n+ <param format="fastqsanger" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ paired reads" help="Must have Sanger-scaled quality values with ASCII offset 33" />\n <expand macro="paired_parameters" />\n </when>\n </conditional>\n@@ -163,32 +162,33 @@\n <when value="preSet" />\n <!-- Full/advanced params. -->\n <when value="full">\n- <param name="read_realign_edit_dist" type="integer" value="1000" label="Max realign edit distance" help="Some of the reads spanning multiple exons may be mapped incorrectly as a contiguous alignment to the genome even though the correct alignment should be a spliced one - this can happen in the presence of processed pseudogenes that are rarely (if at all) transcribed or expressed. This option can direct TopHat to re-align reads for which the edit distance of an alignment obtained in a previous mapping step is above or equal to this option value. If you set this option to 0, TopHat will map every read in all the mapping steps (transcriptome if you provided gene annotations, genome, and finally splice variants detec'..b'ta>\n+ <data format="bam" name="unmapped" label="${tool.name} on ${on_string}: unmapped" from_work_dir="tophat_out/unmapped.bam">\n+ <filter>(params[\'settingsType\'] == \'full\' and params[\'output_unmapped\'])</filter>\n+ <expand macro="dbKeyActions" />\n+ </data>\n+\n </outputs>\n \n <macros>\n <import>tophat_macros.xml</import>\n <xml name="paired_parameters">\n- <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" />\n- <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/>\n+ <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" help="-r/--mate-inner-dist; This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp."/>\n+ <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="--mate-std-dev; The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp."/>\n <!-- Discordant pairs. -->\n- <param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?">\n+ <param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?" help="--no-discordant">\n <option value="No">No</option>\n <option selected="True" value="Yes">Yes</option>\n </param>\n@@ -338,7 +343,7 @@\n <param name="genomeSource" value="indexed" />\n <param name="index" value="tophat_test" />\n <param name="settingsType" value="preSet" />\n- <param name="specReadGroup" value="No" />\n+ <param name="specReadGroup" value="no" />\n <output name="junctions" file="tophat2_out1j.bed" />\n <output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" />\n </test>\n@@ -356,7 +361,7 @@\n <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />\n <param name="mate_inner_distance" value="20" />\n <param name="settingsType" value="preSet" />\n- <param name="specReadGroup" value="No" />\n+ <param name="specReadGroup" value="no" />\n <output name="junctions" file="tophat2_out2j.bed" />\n <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" />\n </test>\n@@ -373,7 +378,7 @@\n <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />\n <param name="mate_inner_distance" value="20" />\n <param name="settingsType" value="preSet" />\n- <param name="specReadGroup" value="No" />\n+ <param name="specReadGroup" value="no" />\n <output name="junctions" file="tophat2_out2j.bed" />\n <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" />\n </test>\n@@ -443,7 +448,7 @@\n </conditional>\n </conditional>\n <conditional name="readGroup">\n- <param name="specReadGroup" value="No" />\n+ <param name="specReadGroup" value="no" />\n </conditional>\n <output name="insertions" file="tophat_out3i.bed" />\n <output name="deletions" file="tophat_out3d.bed" />\n@@ -517,7 +522,7 @@\n </conditional>\n </conditional>\n <conditional name="readGroup">\n- <param name="specReadGroup" value="No" />\n+ <param name="specReadGroup" value="no" />\n </conditional>\n <output name="junctions" file="tophat2_out4j.bed" />\n <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" />\n' |
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| diff -r 6242cda7e278 -r 5c5517d2a9e9 tophat_macros.xml --- a/tophat_macros.xml Thu May 07 15:16:15 2015 -0400 +++ b/tophat_macros.xml Thu May 14 09:39:04 2015 -0400 |
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| @@ -23,14 +23,14 @@ </param> <when value="No"/> <when value="Yes"> - <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> - <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> + <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="--max-insertion-length; The maximum insertion length. The default is 3." /> + <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="--max-deletion-length; The maximum deletion length. The default is 3." /> </when> </conditional> </macro> <macro name="own_junctionsConditional"> <conditional name="own_junctions"> - <param name="use_junctions" type="select" label="Use Own Junctions"> + <param name="use_junctions" type="select" label="Do you want to supply your own junction data" help="The options below allow you validate your own list of known transcripts or junctions with your RNA-Seq data. Note that the chromosome names in the files provided with the options below must match the names in the Bowtie index."> <option value="No">No</option> <option value="Yes">Yes</option> </param> @@ -42,7 +42,7 @@ </param> <when value="No" /> <when value="Yes"> - <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> + <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="-G/--GTF; TopHat with a set of gene model annotations and/or known transcripts, as a GTF 2.2 or GFF3 formatted file. If this option is provided, TopHat will first extract the transcript sequences and use Bowtie to align reads to this virtual transcriptome first. Only the reads that do not fully map to the transcriptome will then be mapped on the genome. The reads that did map on the transcriptome will be converted to genomic mappings (spliced as needed) and merged with the novel mappings and junctions in the final tophat output. Please note that the values in the first column of the provided GTF/GFF file (column which indicates the chromosome or contig on which the feature is located), must match the name of the reference sequence in the Bowtie index you are using with TopHat."/> </when> </conditional> <expand macro="raw_juncsConditional" /> @@ -59,12 +59,12 @@ </param> <when value="No" /> <when value="Yes"> - <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/> + <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="-j/--raw-juncs; Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/> </when> </conditional> </macro> <macro name="no_novel_juncsParam"> - <param name="no_novel_juncs" type="select" label="Only look for supplied junctions"> + <param name="no_novel_juncs" type="select" label="Only look for supplied junctions" help="--no-novel-juncs; Only look for reads across junctions indicated in the supplied GFF or junctions file."> <option value="No">No</option> <option value="Yes">Yes</option> </param> |